PDM

TOPALi now contains two PDM methods - a Pruned PDM method and (the original) non-pruned method, the main difference being that with the pruned method the resultant graphs will show less noise because similar tree topologies are pooled together. Note also, that while running the pruned PDM method, the results can not be viewed in real-time.

A brief overview of the PDM method is available here.

Please ensure that at least 4 sequences have been selected from your alignment before attempting to run PDM. See selecting sequences for further information.

The PDM (Probabilistic Divergence Measures) analysis method is run by selecting Analysis | Run PDM (Jambe) from the menu bar, clicking the Run PDM toolbar button, or pressing Alt-1. This brings up the Probabilistic Divergence Measures - Confirm Settings dialog.

This dialog provides three groups of parameters that can be customized before starting the PDM run.

Basic settings

Basic settings are available by selecting the Basic tabbed pane.

• Step size - step size (in nucleotides) to use when moving along the alignment.
• Window size - window size (in nucleotides) to use when analyzing along the alignment.

Advanced settings

The Advanced tabbed pane allows you to further customize the PDM run.

• Calculate threshold via bootstrapping - calculate threshold via bootstrapping or fast, approximate method - if bootstrapping is selected, then you can also specify the number of threshold runs that will take place
• Number of threshold runs - number of times to re-run the analysis to calculate the threshold values

Bambe settings

The Bambe tabbed pane provides further settings that can be set in order to customize the way in which Bambe runs.

The two most important parameters here are Burn-in time and Cycles.

• Burn-in time - number of cycles to run burn-in algorithm.
• Cycles - number of cycles to run main algorithm.

The higher the value for each of these parameters, the longer the PDM run will take, but the more accurate the results are likely to be.

The remainder of the settings available within here are discussed fully in the accompanying Bambe user manual. Note that this manual lists many settings which are not visible within TOPALi. This is because appropriate values for these settings are estimated automatically by TOPALi and are therefore not available for further customization by the user.

Running PDM

Once you are happy with the settings, click Run to start the PDM run. While PDM is running, the PDM Progress dialog will be displayed.

This dialog provides you with an overview of the following information.

• Local Divergence Measure - displays a graph in real-time that plots the local divergence (statistic) measure. A blue line (representing the current window position) tracks along the graph as the analysis runs.
• Window details - provides details on the current window location, the previous window run time (in seconds), and the estimated time remaining until the run is complete (based on the average window time of all windows processed so far).
• Probability distribution - provides a histogram of the most dominant tree topologies for the current window position. The total number of topologies found so far is provided above the histogram.
• Bambe Details - allow you to view a log of all output produced by Bambe during the current PDM run. Click the Refresh button to update the log.

Once the PDM run is completed, a dialog will inform you of the total time taken.

The PDM results are then displayed within a PDM Results panel. See graphs for further information on this panel and its results.